It is not an easy answer... depends.
Basically, depends on the length of the tunnel.
For a short tunnel, let´s say 5 km, it is just a matter to create a grid on the surface, in top of the tunnel to give coordinates to both entries. Later on, the guide of the tunnel is made by total stations (theodolites anciently) by several methods: English traverse methodology (place benchmarks on pairs, make a traverse until the front of the tunnel in let´s say, par benchmarks and return back on the ones still not used... the problem of it is the turning on the front, but for 5 km is ok), English traverse plus axis (it is the same idea plus an open traverse on the axis of the tunnel, that one allows a better compensation and better results), traverse grids (instead to make observations on just traverse, the observations are made on small 4 point benchmarks grids... that ones is the best and most accurate methodology)
For a long tunnel, the English traverse is not enough, and you should use the 2nd and 3rd methodology.
Anyhow... The study of it should be done before begin, because you can find some surprises... For example, on the Eurotunnel, this question was raised during the construction, and within a few kilometers, the deviation was huge (>50 cm) in both entries (France and England). This deviation was corrected during the remaining tunnel.
There are another factors that are not considered, that it is not just direction... In long tunnels (>25 km) the "gravity" (plumb) it is not the same, so, if you follow the level from both entries, the tunnel will not match on level, and that one should be corrected against the system you are using (normally ellipsoid).
Gyrotheodolites are ok to know the North, but they can not guarantee coordinates, just alignment. So if your coordinates are not matching with a gyrotheodolite... what will you do?
@Fred... the "plumb" system fro tunnels it is just when you are accessing by shafts and when there is no way to place benchmarks or optical plumbs. It is very inaccurate and risky if you down know how to "plumb". Vertical shafts are ok when you have small cover and you have a tunnel without water on top (undersea or under-river tunnels).